Basic cell and molecular
biology
Lecture 1, Cells, genomes and the diversity of life:
The tree of life depicts all the organisms alive and it contain three major domains; the
prokaryotes, eukaryotes and archaea.
Bacteria and archaea can come in all sorts of shapes and sizes. Like spheres (balls),
rod-shaped (sticks), smallest cells (tiny balls/sticks) and spiral (fancy staircase).
Bacteria:
Consists of;
- Outer membrane, consists of a double layer of lipids.
- Cell wall, to separate the interior components of the cell from the exterior
environment. It protects the cell.
- Plasma membrane, also consists of a double layer of lipids.
- DNA, contains all the genetic information of the cell
- Cytoplasm, is a gel-like consistency with the function to transport, maintain cell
structure and to store macromolecules.
- Ribosomes, is made of RNA and proteins, they assemble amino acids to form
proteins.
- A flagellum, the tail of the bacteria which helps it swim.
Extremophiles are microbes who can survive extreme temperature or pressure.
The experiment of Stanley Miller concludes that in prehistoric earth before life was
here, complex organic compounds could be formed. In this time before life, it is
thought that the only chemicals that were abundant in the air were, H2O, H2, CH4 and
NH3. The experiment used a electric arc to simulate the lighting strikes. Out of these
simple chemicals, complex organic compound were created, like hydrogen cyanide,
glycine and alanine.
If genes are duplicated and the two separate genes are given to two different species
the genes are orthologs. But if the separate genes stay in the same species, it is
called paralogs.
Eukaryotic cells:
Eukaryotic cells contain a variety of organelles. One of which is the mitochondria,
which evolved from a symbiotic bacteria, who was absorbed by an ancient archaea.
Plant cells have chloroplasts to do the photosynthesis, these chloroplasts evolved
from symbiotic photosynthesis cells also absorbed by an ancient archaea.
Viruses:
A large percent of all organisms on earth are viruses. There are about 10^31 on earth,
if you stacked all these on top of each other, it would reach 200 lightyears.
Bacteriophage viruses have a head where they store their DNA, and a body which
they use to land on bacteria. Once landed, they penetrate the bacteria and inject it
with the DNA that was stored in the head.
An important experiment was done with this type of virus. It proved that DNA is the
carrier of genetic information and not proteins (which was often thought).
,Model organisms:
- Yeast (Saccharomyces cerevisae); good for research to organelles, DNA replication
and the cell cycle. It is a simple eukaryote with a relative small genome, and strong
genetics. And most importantly, it is cheap to grow.
- Worm (Caenorhabditis elegans); good for research to multicellular development.
- Plant (Arabidopsis thaliana); good for research to plant development and physiology.
It has a relative small genome for a plant, has strong genetics and cheap to grow.
- Fly (Drosophila melanogaster); good for research to genetics. It has strong genetics,
a low frequency of gene duplication and is also cheap.
- Frog (Rana pipiens); good for research of early egg development and cell cycle. It
has big eggs, develops outside of the mother and it duplicates itself without growth.
- Zebrafish (Danio rerio); good for research of vertebrate development. It has strong
genetics and the fish is translucent (see-through).
- Mouse (Mus musculus); good for research of diseases and behavior. It has strong
genetics and if similar to humans.
- Human (Homo sapiens); good for research of diseases and behavior. We have a
large dataset of naturally occurring mutations. For some unknown reason, we are
very interested in this particular species and did a lot of research on it… weird right.
, Lecture 2, Cell chemistry and bioenergetics:
The chemical components of a cell:
- Water is held together by hydrogen bonds.
- There are four types on noncovalent bonds that keep molecules together in cells.
- Some polar molecules form acids and bases in water.
- A cell is formed from carbon compounds.
- Cells contain four major families of small organic molecules.
- The chemistry of cells is dominated by macromolecules with remarkable properties.
- Noncovalent bonds specify both the precise shape of a molecule, as well as it
binding to other molecules.
Energies for cells:
Average thermal motions give the least amount of energy. Then comes the breakage
of non covalent bonds in water. After that is the hydrolysis of ATP in a cell, then the
breakage of a C-C bond. And finally, the complete glucose oxidation creates the most
energy.
Strong acid; gives up its proton (H+) easily.
Weak acid; does not give up its proton easily.
Types of bonds:
Covalent bonds: a covalent bond forms when two atoms come very close together
that they share one or more electrons form the outer shell. A single bond is when they
share two electrons, and a double bond is when they share four electrons.
Ionic bonds: when one atom transfers an electron to another atoms, which cause the
giver to turn positive and the receiver to become negative. These opposite charges
attract each other and form a bond (cute).
Hydrogen bonds: because the O is a little negative charged, and the H a bit positive,
they create a bond together. But alas they are about 20 times weaker then a covalent
bond.
Vanderwaals: in a very short distance any two atoms show a weak bonding because
of the changing electrical charges.
Hydrophobic interactions: when two molecules both are repulsed by water, they
will attract to each other. It is not really a bond, because they don’t link together, but
have a mutual hatred.
biology
Lecture 1, Cells, genomes and the diversity of life:
The tree of life depicts all the organisms alive and it contain three major domains; the
prokaryotes, eukaryotes and archaea.
Bacteria and archaea can come in all sorts of shapes and sizes. Like spheres (balls),
rod-shaped (sticks), smallest cells (tiny balls/sticks) and spiral (fancy staircase).
Bacteria:
Consists of;
- Outer membrane, consists of a double layer of lipids.
- Cell wall, to separate the interior components of the cell from the exterior
environment. It protects the cell.
- Plasma membrane, also consists of a double layer of lipids.
- DNA, contains all the genetic information of the cell
- Cytoplasm, is a gel-like consistency with the function to transport, maintain cell
structure and to store macromolecules.
- Ribosomes, is made of RNA and proteins, they assemble amino acids to form
proteins.
- A flagellum, the tail of the bacteria which helps it swim.
Extremophiles are microbes who can survive extreme temperature or pressure.
The experiment of Stanley Miller concludes that in prehistoric earth before life was
here, complex organic compounds could be formed. In this time before life, it is
thought that the only chemicals that were abundant in the air were, H2O, H2, CH4 and
NH3. The experiment used a electric arc to simulate the lighting strikes. Out of these
simple chemicals, complex organic compound were created, like hydrogen cyanide,
glycine and alanine.
If genes are duplicated and the two separate genes are given to two different species
the genes are orthologs. But if the separate genes stay in the same species, it is
called paralogs.
Eukaryotic cells:
Eukaryotic cells contain a variety of organelles. One of which is the mitochondria,
which evolved from a symbiotic bacteria, who was absorbed by an ancient archaea.
Plant cells have chloroplasts to do the photosynthesis, these chloroplasts evolved
from symbiotic photosynthesis cells also absorbed by an ancient archaea.
Viruses:
A large percent of all organisms on earth are viruses. There are about 10^31 on earth,
if you stacked all these on top of each other, it would reach 200 lightyears.
Bacteriophage viruses have a head where they store their DNA, and a body which
they use to land on bacteria. Once landed, they penetrate the bacteria and inject it
with the DNA that was stored in the head.
An important experiment was done with this type of virus. It proved that DNA is the
carrier of genetic information and not proteins (which was often thought).
,Model organisms:
- Yeast (Saccharomyces cerevisae); good for research to organelles, DNA replication
and the cell cycle. It is a simple eukaryote with a relative small genome, and strong
genetics. And most importantly, it is cheap to grow.
- Worm (Caenorhabditis elegans); good for research to multicellular development.
- Plant (Arabidopsis thaliana); good for research to plant development and physiology.
It has a relative small genome for a plant, has strong genetics and cheap to grow.
- Fly (Drosophila melanogaster); good for research to genetics. It has strong genetics,
a low frequency of gene duplication and is also cheap.
- Frog (Rana pipiens); good for research of early egg development and cell cycle. It
has big eggs, develops outside of the mother and it duplicates itself without growth.
- Zebrafish (Danio rerio); good for research of vertebrate development. It has strong
genetics and the fish is translucent (see-through).
- Mouse (Mus musculus); good for research of diseases and behavior. It has strong
genetics and if similar to humans.
- Human (Homo sapiens); good for research of diseases and behavior. We have a
large dataset of naturally occurring mutations. For some unknown reason, we are
very interested in this particular species and did a lot of research on it… weird right.
, Lecture 2, Cell chemistry and bioenergetics:
The chemical components of a cell:
- Water is held together by hydrogen bonds.
- There are four types on noncovalent bonds that keep molecules together in cells.
- Some polar molecules form acids and bases in water.
- A cell is formed from carbon compounds.
- Cells contain four major families of small organic molecules.
- The chemistry of cells is dominated by macromolecules with remarkable properties.
- Noncovalent bonds specify both the precise shape of a molecule, as well as it
binding to other molecules.
Energies for cells:
Average thermal motions give the least amount of energy. Then comes the breakage
of non covalent bonds in water. After that is the hydrolysis of ATP in a cell, then the
breakage of a C-C bond. And finally, the complete glucose oxidation creates the most
energy.
Strong acid; gives up its proton (H+) easily.
Weak acid; does not give up its proton easily.
Types of bonds:
Covalent bonds: a covalent bond forms when two atoms come very close together
that they share one or more electrons form the outer shell. A single bond is when they
share two electrons, and a double bond is when they share four electrons.
Ionic bonds: when one atom transfers an electron to another atoms, which cause the
giver to turn positive and the receiver to become negative. These opposite charges
attract each other and form a bond (cute).
Hydrogen bonds: because the O is a little negative charged, and the H a bit positive,
they create a bond together. But alas they are about 20 times weaker then a covalent
bond.
Vanderwaals: in a very short distance any two atoms show a weak bonding because
of the changing electrical charges.
Hydrophobic interactions: when two molecules both are repulsed by water, they
will attract to each other. It is not really a bond, because they don’t link together, but
have a mutual hatred.
